Tag Archives: chemistry

Antibiotic synthetic spider silk

I have a couple of questions, what is ‘click’ chemistry and how does a chance meeting lead to a five-year, interdisciplinary research project on synthetic spider silk? From a Jan. 4, 2017 news item on ScienceDaily,

A chance meeting between a spider expert and a chemist has led to the development of antibiotic synthetic spider silk.

After five years’ work an interdisciplinary team of scientists at The University of Nottingham has developed a technique to produce chemically functionalised spider silk that can be tailored to applications used in drug delivery, regenerative medicine and wound healing.

The Nottingham research team has shown for the first time how ‘click-chemistry’ can be used to attach molecules, such as antibiotics or fluorescent dyes, to artificially produced spider silk synthesised by E.coli bacteria. The research, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) is published today in the online journal Advanced Materials.

A Jan. 3, 2016 University of Nottingham press release (also on EurekAlert), which originated the news item, provides a few more details about ‘click’ chemistry (not enough for me) and more information about the research,

The chosen molecules can be ‘clicked’ into place in soluble silk protein before it has been turned into fibres, or after the fibres have been formed. This means that the process can be easily controlled and more than one type of molecule can be used to ‘decorate’ individual silk strands.

Nottingham breakthrough

In a laboratory in the Centre of Biomolecular Sciences, Professor Neil Thomas from the School of Chemistry in collaboration with Dr Sara Goodacre from the School of Life Sciences, has led a team of BBSRC DTP-funded PhD students starting with David Harvey who was then joined by Victor Tudorica, Leah Ashley and Tom Coekin. They have developed and diversified this new approach to functionalising ‘recombinant’ — artificial — spider silk with a wide range of small molecules.

They have shown that when these ‘silk’ fibres are ‘decorated’ with the antibiotic levofloxacin it is slowly released from the silk, retaining its anti-bacterial activity for at least five days.

Neil Thomas, a Professor of Medicinal and Biological Chemistry, said: “Our technique allows the rapid generation of biocompatible, mono or multi-functionalised silk structures for use in a wide range of applications. These will be particularly useful in the fields of tissue engineering and biomedicine.”

Remarkable qualities of spider silk

Spider silk is strong, biocompatible and biodegradable. It is a protein-based material that does not appear to cause a strong immune, allergic or inflammatory reaction. With the recent development of recombinant spider silk, the race has been on to find ways of harnessing its remarkable qualities.

The Nottingham research team has shown that their technique can be used to create a biodegradable mesh which can do two jobs at once. It can replace the extra cellular matrix that our own cells generate, to accelerate growth of the new tissue. It can also be used for the slow release of antibiotics.

Professor Thomas said: “There is the possibility of using the silk in advanced dressings for the treatment of slow-healing wounds such as diabetic ulcers. Using our technique infection could be prevented over weeks or months by the controlled release of antibiotics. At the same time tissue regeneration is accelerated by silk fibres functioning as a temporary scaffold before being biodegraded.”

The medicinal properties of spider silk recognised for centuries.

The medicinal properties of spider silk have been recognised for centuries but not clearly understood. The Greeks and Romans treated wounded soldiers with spider webs to stop bleeding. It is said that soldiers would use a combination of honey and vinegar to clean deep wounds and then cover the whole thing with balled-up spider webs.

There is even a mention in Shakespeare’s Midsummer Night’s Dream: “I shall desire you of more acquaintance, good master cobweb,” the character ‘Bottom’ said. “If I cut my finger, I shall make bold of you.”

The press release goes on to describe the genesis of the project and how this multidisciplinary team was formed in more detail,

The idea came together at a discipline bridging university ‘sandpit’ meeting five years ago. Dr Goodacre says her chance meeting at that event with Professor Thomas proved to be one of the most productive afternoons of her career.

Dr Goodacre, who heads up the SpiderLab in the School of Life Sciences, said: “I got up at that meeting and showed the audience a picture of some spider silk. I said ‘I want to understand how this silk works, and then make some.’

“At the end of the session Neil came up to me and said ‘I think my group could make that.’ He also suggested that there might be more interesting ‘tweaks’ one could make so that the silk could be ‘decorated’ with different, useful, compounds either permanently or which could be released over time due to a change in the acidity of the environment.”

The approach required the production of the silk proteins in a bacterium where an amino acid not normally found in proteins was included. This amino acid contained an azide group which is widely used in ‘click’ reactions that only occur at that position in the protein. It was an approach that no-one had used before with spider silk — but the big question was — would it work?

Dr Goodacre said: “It was the start of a fascinating adventure that saw a postdoc undertake a very preliminary study to construct the synthetic silks. He was a former SpiderLab PhD student who had previously worked with our tarantulas. Thanks to his ground work we showed we could produce the silk proteins in bacteria. We were then joined by David Harvey, a new PhD student, who not only made the silk fibres, incorporating the unusual amino acid, but also decorated it and demonstrated its antibiotic activity. He has since extended those first ideas far beyond what we had thought might be possible.”

David Harvey’s work is described in this paper but Professor Thomas and Dr Goodacre say this is just the start. There are other joint SpiderLab/Thomas lab students working on uses for this technology in the hope of developing it further.

David Harvey, the lead author on this their first paper, has just been awarded his PhD and is now a postdoctoral researcher on a BBSRC follow-on grant so is still at the heart of the research. His current work is focused on driving the functionalised spider silk technology towards commercial application in wound healing and tissue regeneration.

Here’s a link to and a citation for the paper,

Antibiotic Spider Silk: Site-Specific Functionalization of Recombinant Spider Silk Using “Click” Chemistry by David Harvey, Philip Bardelang, Sara L. Goodacre, Alan Cockayne, and Neil R. Thomas. Advanced Materials DOI: 10.1002/adma.201604245 Version of Record online: 28 DEC 2016

© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

I imagine Mr. Cockayne’s name has led to much teasing over the years. People who have names with that kind of potential tend to either change them or double down and refuse to compromise.

“One minus one equals zero” has been disproved

Two mirror-image molecules can be optically active according to an April 27, 2016 news item on ScienceDaily,

In 1848, Louis Pasteur showed that molecules that are mirror images of each other had exactly opposite rotations of light. When mixed in solution, they cancel the effects of the other, and no rotation of light is observed. Now, a research team has demonstrated that a mixture of mirror-image molecules crystallized in the solid state can be optically active.

An April 26, 2016 Northwestern University news release (also on EurekAlert), which originated the news item, expands on the theme,

In the world of chemistry, one minus one almost always equals zero.

But new research from Northwestern University and the Centre National de la Recherche Scientifique (CNRS) in France shows that is not always the case. And the discovery will change scientists’ understanding of mirror-image molecules and their optical activity.

Now, Northwestern’s Kenneth R. Poeppelmeier and his research team are the first to demonstrate that a mixture of mirror-image molecules crystallized in the solid state can be optically active. The scientists first designed and made the materials and then measured their optical properties.

“In our case, one minus one does not always equal zero,” said first author Romain Gautier of CNRS. “This discovery will change scientists’ understanding of these molecules, and new applications could emerge from this observation.”

The property of rotating light, which has been known for more than two centuries to exist in many molecules, already has many applications in medicine, electronics, lasers and display devices.

“The phenomenon of optical activity can occur in a mixture of mirror-image molecules, and now we’ve measured it,” said Poeppelmeier, a Morrison Professor of Chemistry in the Weinberg College of Arts and Sciences. “This is an important experiment.”

Although this phenomenon has been predicted for a long time, no one — until now — had created such a racemic mixture (a combination of equal amounts of mirror-image molecules) and measured the optical activity.

“How do you deliberately create these materials?” Poeppelmeier said. “That’s what excites me as a chemist.” He and Gautier painstakingly designed the material, using one of four possible solid-state arrangements known to exhibit circular dichroism (the ability to absorb differently the “rotated” light).

Next, Richard P. Van Duyne, a Morrison Professor of Chemistry at Northwestern, and graduate student Jordan M. Klingsporn measured the material’s optical activity, finding that mirror-image molecules are active when arranged in specific orientations in the solid state.

Here’s a link to and a citation for the paper,

Optical activity from racemates by Romain Gautier, Jordan M. Klingsporn, Richard P. Van Duyne, & Kenneth R. Poeppelmeier. Nature Materials (2016) doi:10.1038/nmat4628 Published online 18 April 2016

This paper is behind a paywall.

Making perfume molecules last longer

If the thought of having expensive perfume last longer is appealing then this research will pique your interest. From a Feb. 17, 2016 American Chemical Society (ACS) news release, also on EurekAlert, (Note: Links have been removed),

Fragrances can be powerful. They can sooth or revitalize, evoke the forest or sea, and remind us of the past. To capture them, manufacturers infuse scents into products from toilet bowl cleaners to luxury perfumes. But once released from a bottle, fragrances evaporate quickly. Now researchers report in the journal ACS Applied Materials & Interfaces a new way to encapsulate fragrance molecules to make a product’s scent last.

The challenge with creating long-lasting fragrances is that aroma molecules tend to be small and volatile. That means they can sneak through barriers easily and disperse quickly. Some methods have been developed to prevent fragrance molecules from hastily escaping from a spritz of perfume or a dollop of lotion. For example, one process slows down the molecules by packaging them in microcapsules. But the technique is inefficient and doesn’t control for shell size, thickness or structure, which makes it harder to work with. David A. Weitz and colleagues wanted to figure out a new strategy using microfluidic and bulk emulsification to encapsulate fragrances.

First, to get a homogeneous mixture of water and α-pinene molecules — found in oils from pine trees and rosemary — the researchers emulsified them (think blending together two ingredients like oil and vinegar that normally separate). Pumping the emulsion into tiny glass microfluidic tubes created uniform microcapsules. Testing showed that the capsules successfully slowed the release of α-pinene. In addition to its use in the fragrance industry, the researchers say the technique could have applications in drug delivery or other areas.

The authors acknowledge funding from Procter & Gamble Co., the National Science Foundation, the Harvard Materials Research Science and Engineering Center, and the National Research Foundation of Korea.

Here’s a link to and a citation for the paper,

Encapsulation and Enhanced Retention of Fragrance in Polymer Microcapsules by Hyomin Lee, Chang-Hyung Choi, Alireza Abbaspourrad, Chris Wesner, Marco Caggioni, Taotao Zhu, and David A. Weitz. ACS Appl. Mater. Interfaces, 2016, 8 (6), pp 4007–4013 DOI: 10.1021/acsami.5b11351 Publication Date (Web): January 22, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Green tech with single atom platinum catalyst?

There’s something mind boggling to me about the notion of a single atom catalyst. Luckily, an Oct. 5, 2015 news item on Nanowerk describes the research (Note: A link has been removed),

A new generation of platinum-copper catalysts that require very low concentrations of platinum in the form of individual atoms to cleanly and cheaply perform important chemical reactions is reported today by Tufts University researchers in the journal Nature Communications (“Selective hydrogenation of butadiene on platinum copper alloys at the single atom limit”).

An Oct. 9, 2015 Tufts University news release on EurekAlert, which originated the news item, describes the nature of the problem the researchers were trying to resolve and their solution,

Platinum is used as a catalyst in fuel cells, in automobile converters and in the chemical industry because of its remarkable ability to facilitate a wide range of chemical reactions. However, its future potential uses are significantly limited by scarcity and cost, as well as the fact that platinum readily binds with carbon monoxide, which “poisons” the desired reactions, for example in polymer electrolyte membrane (PEM) fuel cells, which are the leading contenders for small-scale and mobile power generation not based on batteries or combustion engines.

The Tufts researchers discovered that dispersing individual, isolated platinum atoms in much less costly copper surfaces can create a highly effective and cost-efficient catalyst for the selective hydrogenation of 1,3 butadiene, a chemical produced by steam cracking of naphtha or by catalytic cracking of gas oil. Butadiene is an impurity in propene streams that must be removed from the stream through hydrogenation in order to facilitate downstream polymer production. The current industrial catalyst for butadiene hydrogenation uses palladium and silver.

Like Sugar in Coffee

Copper, while a relatively cheap metal, is not nearly as catalytically powerful as platinum, noted Professor of Chemistry Charles Sykes, Ph.D., one of the senior authors on the paper. “We wanted to find a way to improve its performance.”

The researchers first conducted surface science experiments to study precisely how platinum and copper metals mix. “We were excited to find that the platinum metal dissolved in copper, just like sugar in hot coffee, all the way down to single atoms. We call such materials single atom alloys,” said Sykes.

The Tufts chemists used a specialized low temperature scanning tunneling microscope to visualize the single platinum atoms and their interaction with hydrogen. “We found that even at temperatures as low as minus 300 degrees F these platinum atoms were capable of splitting hydrogen molecules into atoms, indicating that the platinum atoms would be very good at activating hydrogen for a chemical reaction,” Sykes said.

With that knowledge, Sykes and his fellow chemists turned to long-time Tufts collaborator Maria Flytzani-Stephanopoulos, Ph.D., the Robert and Marcy Haber Endowed Professor in Energy Sustainability at the School of Engineering, to determine which hydrogenation reaction would be most significant for industrial applications. The answer, she said, was butadiene.

The model catalyst performed effectively for that reaction in vacuum conditions in the laboratory, so Flytzani-Stephanopoulos’s team took the study to the next level. They synthesized small quantities of realistic catalysts, such as platinum-copper single atom alloy nanoparticles supported on an alumina substrate, and then tested them under industrial pressure and temperatures.

“To our delight, these catalysts worked very well and their performance was steady for many days,” said Flytzani-Stephanopoulos. “While we had previously shown that palladium would do related reactions in a closed reactor system, this work with platinum is our first demonstration of operation in a flow reactor at industrially relevant conditions. We believe this approach is also applicable to other precious metals if added as minority components in copper.”

Further, the researchers found that the reaction actually became less efficient when they used more platinum, because clusters of platinum atoms have inferior selectivity compared with individual atoms. “In this case, less is more,” said Flytzani-Stephanopoulos, “which is a very good thing.”

Environmental Benefits

Because platinum is at the center of many clean energy and green chemicals production technologies, such as fuel cells, catalytic converters, and value-added chemicals from bio-renewable feedstocks, the new, less expensive platinum-copper catalysts could facilitate broader adoption of such environmentally friendly devices and processes, she added.

The news release goes on to describe this cross-disciplinary partnership,

The work is the latest fruit from a long cross-disciplinary partnership between Sykes and Flytzani-Stephanopoulos.

“Maria and I met more than seven years ago and talked regularly about how to combine our fairly different fields of research into an effective collaboration across the schools of Arts and Sciences and Engineering,” said Sykes. “I had a state-of-the-art microscope that could see and manipulate atoms and molecules, and I wanted to use its unique capabilities to gain insight into industrially important chemical reactions. In the early 2000s, Maria’s group had pioneered the single-atom approach for metals anchored on oxide supports as the exclusive active sites for the water-gas shift reaction to upgrade hydrogen streams for fuel cell use. Catalyst design know-how already existed in her lab. In retrospect, it seems obvious that combining forces would be a ‘natural’ development. Together we embarked on a new direction involving single atom alloys as catalysts for selective hydrogenation reactions. Our microscope was uniquely suited for characterizing the atomic composition of surfaces. We got funding from the National Science Foundation, U.S. Department of Energy and the Tufts Collaborates initiative to pursue this new area of research.”

Sykes and Flytzani-Stephanopoulos have used this approach to design a variety of single atom alloy catalysts that have, in the last two years, sparked international interest.

“Traditionally catalyst development happens by trial and error and screening many materials,” said Flytzani-Stephanopoulos. “In this study we took a fundamental approach to understanding the atomic scale structure and properties of single atom alloy surfaces and then applied this knowledge to develop a working catalyst. Armed with this knowledge, we are now ready to compare the stability of these single atom alloy catalysts to single atom catalysts supported on various oxide or carbon surfaces. This may give us very useful criteria for industrial catalyst design.”

Here’s a link to and a citation for the paper,

Selective hydrogenation of 1,3-butadiene on platinum–copper alloys at the single-atom limit by Felicia R. Lucci, Jilei Liu, Matthew D. Marcinkowski, Ming Yang, Lawrence F. Allard, Maria Flytzani-Stephanopoulos, & E. Charles H. Sykes. Nature Communications 6, Article number: 8550 doi:10.1038/ncomms9550 Published 09 October 2015

This is an open access paper.

Molecules (arynes) seen for first time in 113 years

Arynes were first theorized in 1902 and they’ve been used as building blocks to synthesize a variety of compounds but they’re existence hasn’t been confirmed until now.

AFM image of an aryne molecule imaged with a CO tip. Courtesy: IBM

AFM image of an aryne molecule imaged with a CO tip. Courtesy: IBM

A July 13, 2015 news item in Nanowerk makes the announcement (Note: A link has been removed),

chemistry teachers and students can breath a sigh of relief. After teaching and learning about a particular family of molecules for decades, scientists have finally proven that they do in fact exist.

In a new paper published online today in Nature Chemistry (“On-surface generation and imaging of arynes by atomic force microscopy”), scientists from IBM Research and CIQUS at the University of Santiago de Compostela, Spain, have confirmed the existence and characterized the structure of arynes, a family of highly-reactive short-lived molecules which was first suggested 113 years ago. The technique has broad applications for on-surface chemistry and electronics, including the preparation of graphene nanoribbons and novel single-molecule devices.

A July 13, 2015 IBM news release by Chris Sciacca, which originated the news item, describes arynes and the imaging process used to capture them for the first time (Note: Links have been removed),

“Arynes are discussed in almost every undergraduate course on organic chemistry around the world. Therefore, it’s kind of a relief to find the final confirmation that these molecules truly exist,” said Prof. Diego Peña, a chemist at the University of Santiago de Compostela.

“I look forward to seeing new chemical challenges solved by the combination of organic synthesis and atomic force microscopy.”

There are trillions of molecules in the universe and some of them are stable enough to be isolated and characterized, but many others are so short-lived that they can only be proposed indirectly, via chemical reactions or spectroscopic methods.

One such species are arynes, which were first suggested in 1902, and since then have been used as intermediates or building blocks in the synthesis of a variety of compounds for applications including medicine, organic electronics and molecular materials. The challenge with these particular molecules is that they only exist for several milliseconds making them extremely challenging to image, until now.

The imaging was accomplished by means of atomic force microscopy (AFM), a scanning technique that can accomplish nanometer-level resolution. After the preparation of the key aryne precursor by CIQUS, IBM scientists used the sharp tip of a scanning tunneling microscope (STM) to generate individual aryne molecules from precursor molecules by atomic manipulation. The experiments were performed on films of sodium chloride, at temperatures near absolute zero, to stabilize the aryne.

Once the molecules were isolated, the team used AFM to measure the tiny forces between the STM tip, which is terminated with a single carbon monoxide molecule, and the sample to image the aryne’s molecular structure. The resulting image was so clear that the scientists could study their chemical nature based on the minute differences between individual bonds.

“Our team has developed several state-of-the-art techniques since 2009, which made this achievement possible,” said Dr. Niko Pavliček, a physicist at IBM Research – Zurich and lead author of the paper. “For this study, it was absolutely essential to pick an insulating film on which the molecules were adsorbed and to deliberately choose the atomic tip-terminations to probe them. We hope this technique will have profound effects on the future of chemistry and electronics.”

Prof. Peña, added that “These findings on arynes can be compared with the long-standing search for the giant squid. For centuries, fishermen had found clues of the existence of this legendary animal. But it was only very recently that scientists managed to film a giant squid alive. In both cases, state-of-the-art technologies were crucial to observe these elusive species alive: a low-noise submarine for the giant squid; a low-temperature AFM for the aryne.”

This research is part of IBM’s five-year, $3 billion investment to push the limits of chip technology and semiconductor innovations needed to meet the emerging demands of cloud computing and Big Data systems.

This work is a result of the large European project called (Planar Atomic and Molecular Scale Devices). PAMS’ main objective is to develop and investigate novel electronic devices of nanometric-scale size. Part of this research is also funded by a European Research Council Advanced Grant awarded to IBM scientist Gerhard Meyer, who is also a co-author of the paper.

Here’s a link to and a citation for the paper,

On-surface generation and imaging of arynes by atomic force microscopy by Niko Pavliček, Bruno Schuler, Sara Collazos, Nikolaj Moll, Dolores Pérez, Enrique Guitián, Gerhard Meyer, Diego Peña, & Leo Gross. Nature Chemistry (2015) doi:10.1038/nchem.2300 Published online 13 July 2015

This paper is behind a paywall.

The science of the Avengers: Age of Ultron

The American Chemical Society (ACS) has produced a video (almost 4 mins.) in their Reactions Science Video Series of podcasts focusing on the Avengers, super heroes, as portrayed in Avengers: Age of Ultron and science. From an April 29, 2015 ACS news release on EurekAlert,

Science fans, assemble! On May 1, the world’s top superhero team is back to save the day in “Avengers: Age of Ultron.” This week, Reactions looks at the chemistry behind these iconic heroes’ gear and superpowers, including Tony Stark’s suit, Captain America’s shield and more.

Here’s the video,

While the chemists are interested in the metal alloys, there is more ‘super hero science’ writing out there. Given my interests, I found the ‘Captain America’s shield as supercapacitor theory’ as described in Matt Shipman’s April 15, 2014 post on The Abstract (North Carolina State University’s official newsroom blog quite interesting. I featured Shipman’s ‘super hero and science’ series of posts in my April 28, 2014 posting.

Gold atoms: sometimes they’re a metal and sometimes they’re a molecule

Fascinating work out of Finland shows that a minor change in the number of gold atoms in your gold nanoparticle can mean the difference between a metal and a molecule (coincidentally, this phenomenon is alluded to in my April 14, 2015 post (Nature’s patterns reflected in gold nanoparticles); more about that at the end of this piece. Getting back to Finland and when gold is metal and when it’s a molecule, here’s more from an April 10, 2015 news item on ScienceDaily,

Researchers at the Nanoscience Center at the University of Jyväskylä, Finland, have shown that dramatic changes in the electronic properties of nanometre-sized chunks of gold occur in well-defined size range. Small gold nanoclusters could be used, for instance, in short-term storage of energy or electric charge in the field of molecular electronics. Funded by the Academy of Finland, the researchers have been able to obtain new information which is important, among other things, in developing bioimaging and sensing based on metal-like clusters.

An April 10, 2015 news release (also on EurekAlert) on the Academy of Finland (Suomen Akatemia) website, which originated the news item, describes the work in more detail,

Two recent papers by the researchers at Jyväskylä (1, 2) demonstrate that the electronic properties of two different but still quite similar gold nanoclusters can be drastically different. The clusters were synthesised by chemical methods incorporating a stabilising ligand layer on their surface. The researchers found that the smaller cluster, with up to 102 gold atoms, behaves like a giant molecule while the larger one, with at least 144 gold atoms, already behaves, in principle, like a macroscopic chunk of metal, but in nanosize.

The fundamentally different behaviour of these two differently sized gold nanoclusters was demonstrated by shining a laser light onto solution samples containing the clusters and by monitoring how energy dissipates from the clusters into the surrounding solvent.

“Molecules behave drastically different from metals,” said Professor Mika Pettersson, the principal investigator of the team conducting the experiments. “The additional energy from light, absorbed by the metal-like clusters, transfers to the environment extremely rapidly, in about one hundred billionth of a second, while a molecule-like cluster is excited to a higher energy state and dissipates the energy into the environment with a rate that is at least 100 times slower. This is exactly what we saw: the 102-gold atom cluster is a giant molecule showing even a transient magnetic state while the 144-gold atom cluster is already a metal. We’ve thus managed to bracket an important size region where this fundamentally interesting change in the behaviour takes place.”

“These experimental results go together very well with what our team has seen from computational simulations on these systems,” said Professor Hannu Häkkinen, a co-author of the studies and the scientific director of the nanoscience centre. “My team predicted this kind of behaviour back in 2008-2009 when we saw big differences in the electronic structure of exactly these nanoclusters. It’s wonderful that robust spectroscopic experiments have now proved these phenomena. In fact, the metal-like 144-atom cluster is even more interesting, since we just published a theoretical paper where we saw a big enhancement of the metallic properties of just a few copper atoms mixed with gold.” (3)

Here are links to and citation for the papers,

Ultrafast Electronic Relaxation and Vibrational Cooling Dynamics of Au144(SC2H4Ph)60 Nanocluster Probed by Transient Mid-IR Spectroscopy by Satu Mustalahti, Pasi Myllyperkiö, Tanja Lahtinen, Kirsi Salorinne, Sami Malola, Jaakko Koivisto, Hannu Häkkinen, and Mika Pettersson. J. Phys. Chem. C, 2014, 118 (31), pp 18233–18239 DOI: 10.1021/jp505464z Publication Date (Web): July 3, 2014

Copyright © 2014 American Chemical Society

Copper Induces a Core Plasmon in Intermetallic Au(144,145)–xCux(SR)60 Nanoclusters by Sami Malola, Michael J. Hartmann, and Hannu Häkkinen. J. Phys. Chem. Lett., 2015, 6 (3), pp 515–520 DOI: 10.1021/jz502637b Publication Date (Web): January 22, 2015

Copyright © 2015 American Chemical Society

Molecule-like Photodynamics of Au102(pMBA)44 Nanocluster by Satu Mustalahti, Pasi Myllyperkiö, Sami Malola, Tanja Lahtinen, Kirsi Salorinne, Jaakko Koivisto, Hannu Häkkinen, and Mika Pettersson. ACS Nano, 2015, 9 (3), pp 2328–2335 DOI: 10.1021/nn506711a Publication Date (Web): February 22, 2015

Copyright © 2015 American Chemical Society

These papers are behind paywalls.

As for my April 14, 2015 post (Nature’s patterns reflected in gold nanoparticles), researchers at Carnegie Mellon University were researching patterns in different sized gold nanoparticles when this was noted in passing,

… Normally, gold is one of the best conductors of electrical current, but the size of Au133 is so small that the particle hasn’t yet become metallic. …

Beginner’s guide to gold nanoparticles in an Academic Minute

Catherine J Murphy, professor of chemistry at the University of Illinois at Urbana-Champaign (UIUC), contributed to Inside Higher Education’s Academic Minute audio podcast series according to an April 9, 2015 news item on the organization’s website.

Murphy provides a very good beginner’s description of gold nanoparticles.

Inside Higher Education offers a transcript of the ‘minute’ by Matthew on its Academic Minute website’s Catherine Murphy webpage,

Introduction: Atomic element #79 is the precious metal more commonly known as gold.

Transcript: Nanotechnology is the study of matter on the 1-100 nanometer scale – about ten to a thousand atoms across. Many elements in the periodic table are metals, and chemists like me are figuring out ways to create tiny metal nanoparticles of different shapes and sizes – spheres, cylinders, stars, you name it. We focus on gold. The cool thing is that each shape and size of gold nanoparticle absorbs and scatters light at different wavelengths, so each size and shape has a different color. So all the colors of the rainbow, and then some, are possible with gold nanoparticles.

The reasons for these neat colors go back to understanding the fundamental nature of light. We know from Maxwell’s equations that light is an electromagnetic wave. If light impinges on a “small conducting sphere,” then there are conditions under which certain wavelengths of light lead to huge oscillations in the electron cloud around the metal, for any metal in the periodic table, as a function of the size of the sphere, the dielectric constant of the metal, and the refractive index of the medium. These equations were worked out by Gustav Mie in the early 1900’s and give us a fundamental understanding of where these brilliant colors come from. In the last 30 years, scientists have adapted his equation for all kinds of shapes beyond spheres.

But gold nanoparticles are not just pretty to look at: they can do a lot of interesting things. For instance, these gold nanoparticles also scatter light, making them easy to find in a simple optical microscope; and since gold is environmentally benign compared to other metals, people are using gold nanoparticles to image biological systems. When you shine light on gold, the absorption of light is very strong at the right wavelengths. Once the particles have absorbed all this energy, what do they do with it? They dump it out as heat to the environment, and so can raise the temperature of their surroundings by many degrees. This is the basis for what scientists call “photothermal therapy,” the idea that if you could target gold nanoparticles to cancer cells, or pathogens, then you could shine light at the wavelength you desire and kill the cancer cells or pathogens. Finally, if you make gold nanoparticles really really small, like 10 atoms across, they no longer act like a noble, unreactive metal at all; they become very active catalysts, like the catalytic converter in your car. So chemists are also very interested in figuring out the transition between unreactive and reactive nanoparticles.

For anyone who might be interested in the series, the Academic Minute covers a wide variety of topics ranging from ‘addiction vaccines’ to ‘digital transgender archives’ to ‘aeroponic gardening’ to ‘a science of the voice’ to ‘Viking social standing’ and more. The series seems to have been started in January 2011 and they’ve been adding to the list of podcasts at a lively rate (lately, it’s one per day). There are over 200 pages of audio podcasts available for your listening pleasure.

The quantum chemistry of nanomedicines

A Jan. 29, 2015 news item on Nanowerk provides an overview of the impact quantum chemical reactions may have on nanomedicines. Intriguingly, this line of query started with computations of white dwarf stars,

Quantum chemical calculations have been used to solve big mysteries in space. Soon the same calculations may be used to produce tomorrow’s cancer drugs.

Some years ago research scientists at the University of Oslo in Norway were able to show that the chemical bonding in the magnetic fields of small, compact stars, so-called white dwarf stars, is different from that on Earth. Their calculations pointed to a completely new bonding mechanism between two hydrogen atoms. The news attracted great attention in the media. The discovery, which in fact was made before astrophysicists themselves observed the first hydrogen molecules in white dwarf stars, was made by UiO’s Centre for Theoretical and Computational Chemistry. They based their work on accurate quantum chemical calculations of what happens when atoms and molecules are exposed to extreme conditions.

A Jan. 29, 2015 University of Oslo press release by Yngve Vogt, which originated the news item, offers a substantive description of molecules, electrons, and more for those of us whose last chemistry class is lost in the mists of time,

The research team is headed by Professor Trygve Helgaker, who for the last thirty years has taken the international lead on the design of a computer system for calculating quantum chemical reactions in molecules.

Quantum chemical calculations are needed to explain what happens to the electrons’ trajectories within a molecule.

Consider what happens when UV radiation sends energy-rich photons into your cells. This increases the energy level of the molecules. The outcome may well be that some of the molecules break up. This is exactly what happens when you sun-bathe.

“The extra energy will affect the behaviour of electrons and can destroy the chemical bonding within the molecule. This can only be explained by quantum chemistry. The quantum chemical models are used to produce a picture of the forces and tensions at play between the atoms and the electrons of a molecule, and of what is required for a molecule to dissociate,” says Trygve Helgaker.

The absurd world of the electrons

The quantum chemical calculations solve the Schrödinger equation for molecules. This equation is fundamental to all chemistry and describes the whereabouts of all electrons within a molecule. But here we need to pay attention, for things are really rather more complicated than that. Your high school physics teacher will have told you that electrons circle the atom. Things are not that simple, though, in the world of quantum physics. Electrons are not only particles, but waves as well. The electrons can be in many places at the same time. It’s impossible to keep track of their position. However, there is hope. Quantum chemical models describe the electrons’ statistical positions. In other words, they can establish the probable location of each electron.

The results of a quantum chemical calculation are often more accurate than what is achievable experimentally.

Among other things, the quantum chemical calculations can be used to predict chemical reactions. This means that the chemists will no longer have to rely on guesstimates in the lab. It is also possible to use quantum chemical calculations in order to understand what happens in experiments.

Enormous calculations

The calculations are very demanding.

“The Schrödinger equation is a highly complicated, partial differential equation, which cannot be accurately solved. Instead, we need to make do with heavy simulations”, says researcher Simen Kvaal.

The computations are so demanding that the scientists use one of the University’s fastest supercomputers.

“We are constantly stretching the boundaries of what is possible. We are restricted by the available machine capacity,” explains Helgaker.

Ten years ago it took two weeks to carry out the calculations for a molecule with 140 atoms. Now it can be done in two minutes.

“That’s 20,000 times faster than ten years ago. The computation process is now running 200 times faster because the computers have been doubling their speed every eighteen months. And the process is a further 100 times faster because the software has been undergoing constant improvement,” says senior engineer Simen Reine.

This year the research group has used 40 million CPU hours, of which twelve million were on the University’s supercomputer, which is fitted with ten thousand parallel processors. This allows ten thousand CPU hours to be over and done with in 60 minutes.

“We will always fill the computer’s free capacity. The higher the computational capacity, the bigger and more reliable the calculations.”

Thanks to ever faster computers, the quantum chemists are able to study ever larger molecules.

Today, it’s routine to carry out a quantum chemical calculation of what happens within a molecule of up to 400 atoms. By using simplified models it is possible to study molecules with several thousand atoms. This does, however, mean that some of the effects within the molecule are not being described in detail.

The researchers are now getting close to a level which enables them to study the quantum mechanics of living cells.

“This is exciting. The molecules of living cells may contain many hundred thousand atoms, but there is no need to describe the entire molecule using quantum mechanical principles. Consequently, we are already at a stage when we can help solve biological problems.”

There’s more from the press release which describes how this work could be applied in the future,

Hunting for the electrons of the insulin molecule

The chemists are thus able to combine sophisticated models with simpler ones. “This will always be a matter of what level of precision and detail you require. The optimal approach would have been to use the Schrödinger equation for everything.”

By way of compromise they can give a detailed description of every electron in some parts of the model, while in other parts they are only looking at average numbers.

Simen Reine has been using the team’s computer program, while working with Aarhus University [Finland], on a study of the insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons.

“All electrons repel each other, while at the same time being pulled towards the atomic nuclei. The nuclei also repel each other. Nevertheless, the molecule remains stable. In order to study a molecule to a high level of precision, we therefore need to consider how all of the electrons move relative to one another. Such calculations are referred to as correlated and are very reliable.”

A complete correlated calculation of the insulin molecule takes nearly half a million CPU hours. If they were given the opportunity to run the program on the entire University’s supercomputer, the calculations would theoretically take two days.

“In ten years, we’ll be able to make these calculations in two minutes.”

Medically important

“Quantum chemical calculations can help describe phenomena at a level that may be difficult to access experimentally, but may also provide support for interpreting and planning experiments. Today, the calculations will be put to best use within the fields of molecular biology and biochemistry,” says Knut Fægri [vice-rector at the University of Oslo].

“Quantum chemistry is a fundamental theory which is important for explaining molecular events, which is why it is essential to our understanding of biological systems,” says [Associate Professor] Michele Cascella.

By way of an example, he refers to the analysis of enzymes. Enzymes are molecular catalysts that boost the chemical reactions within our cells.

Cascella also points to nanomedicines, which are drugs tasked with distributing medicine round our bodies in a much more accurate fashion.

“In nanomedicine we need to understand physical phenomena on a nano scale, forming as correct a picture as possible of molecular phenomena. In this context, quantum chemical calculations are important,” explains Michele Cascella.

Proteins and enzymes

Professor K. Kristoffer Andersson at the Department of Biosciences uses the simpler form of quantum chemical calculations to study the details of protein structures and the chemical atomic and electronic functions of enzymes.

“It is important to understand the chemical reaction mechanism, and how enzymes and proteins work. Quantum chemical calculations will teach us more about how proteins go about their tasks, step by step. We can also use the calculations to look at activation energy, i.e. how much energy is required to reach a certain state. It is therefore important to understand the chemical reaction patterns in biological molecules in order to develop new drugs,” says Andersson.

His research will also be useful in the search for cancer drugs. He studies radicals, which may be important to cancer. Among other things, he is looking at the metal ions function in proteins. These are ions with a large number of protons, neutrons and electrons.


Professor Einar Uggerud at the Department of Chemistry has uncovered an entirely new form of chemical bonding through sophisticated experiments and quantum chemical calculations.

Working with research fellow Glenn Miller, Professor Uggerud has found an unusually fragile key molecule, in a kite-shaped structure, consisting of magnesium, carbon and oxygen. The molecule may provide a new understanding of photosynthesis. Photosynthesis, which forms the basis for all life, converts CO2 into sugar molecules.

The molecule reacts so fast with water and other molecules that it has only been possible to study in isolation from other molecules, in a vacuum chamber.

“Time will tell whether the molecule really has an important connection with photosynthesis,” says Einar Uggerud.

I’m delighted with this explanation as it corrects my understanding of chemical bonds and helps me to better understand computational chemistry. Thank you University of Oslo and Yngve Vogt.

Finally, here’s a representation of an insulin molecule as understood by quantum computation,


INSULIN: Working with Aarhus University, Simen Reine has calculated the tensions between the electrons and atoms of an insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons. Illustration: Simen Reine-UiO


Licking your way to new ice cream: a physicist’s ice cream changes colour when licked

Bob Yirkas in a July 20, 2014 article for phys.org describes a new twist on ice cream,

Spanish physicist, engineer, professor and ice cream lover Manuel Linares has together with a couple of colleagues created an ice cream that changes colors when it’s licked—in a cone. Not content with the life of a physics professor, Linares signed up for training with Asociación Empresarial Nacional de Elaboradores Artesanos y Comerciantes de Helados y Horchatas—a craftsmen and businessmen association in Spain that offers mentored coursework.

Linares pursued what he has described as a “Masters Diploma in Creating Artisan Ice Cream.” Intrigued by the ice that changes color under fluorescent lights, created by Charlie Francis, Linares set his sights on figuring out a way to create a type of ice cream that would change color in response to temperature changes and acids found in the human mouth. He enlisted the assistance of a couple of unnamed buddies and they all got to work in a lab that Linares put together with his own funds. Linares has told the press that it took the three of them just one week to come up with the color changing ice cream. The final product, which reportedly has a similar taste to tutti-frutti, has been named Xamaleón.

Mariella Moon’s July 30, 2014 article for Engadget reveals more about Linares’ iice cream confection and his future plans,

He [Linares] calls it the Xamaleón, a play on the Spanish word for chameleon, and it originally starts as a periwinkle blue frozen treat until it’s spritzed with Linares’ “love elixir,” a super secret mixture he concocted himself. This mixture reacts to changes in temperature and saliva, causing the tutti-frutti-flavored ice cream to turn into purple, then into pink as you lick.

As unusual as it sounds, this is just the beginning of Linares’ foray into the color-changing ice cream business: he also plans to whip up ice cream that turns from white to pink, and another one that glows under ultraviolet light. You can only get a scoop of this chameleon ice cream from one [of] the creator’s shops in Spain right now, …

The earliest version of this story that I can find is a July 16, 2014 article by Carme Gasull for Cocinatis. You will need Spanish language skills to read it but luckily, this photograph included in the article speaks for itself,

Xamaleón [downloaded from http://www.cocinatis.com/comer/xamaleon-helado-que-cambia-color_2014071600015.html]

Xamaleón [downloaded from http://www.cocinatis.com/comer/xamaleon-helado-que-cambia-color_2014071600015.html]

This is Xamaleón’s pre-love elixir spritz periwinkle blue. You can find more pictures (and a video too) of the ice cream in various stages of its colourful transformation by following this posting’s links to other articles or, if you choose, to search, there’s a lot of material as this has been a very popular topic. BTW, July was National Ice Cream Month as per this July 1, 2014 posting by Anthony Selden for daily.com.